+Open data
-Basic information
Entry | Database: PDB / ID: 4fqe | ||||||
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Title | KdgM porin | ||||||
Components | Oligogalacturonate-specific porin kdgM | ||||||
Keywords | MEMBRANE PROTEIN / beta barrel / porin / outer membrane protein / oligogalacturonate specificity | ||||||
Function / homology | Function and homology information pectin metabolic process / voltage-gated monoatomic ion channel activity / porin activity / pore complex / carbohydrate transport / cell outer membrane Similarity search - Function | ||||||
Biological species | Dickeya dadantii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Hutter, C. / Peneff, C.M. / Wirth, C. / Schirmer, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structure of the oligogalacturonate-specific KdgM porin. Authors: Hutter, C.A. / Lehner, R. / Wirth, C.h. / Condemine, G. / Peneff, C. / Schirmer, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fqe.cif.gz | 93.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fqe.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 4fqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fqe_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4fqe_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4fqe_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 4fqe_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/4fqe ftp://data.pdbj.org/pub/pdb/validation_reports/fq/4fqe | HTTPS FTP |
-Related structure data
Related structure data | 4pr7C 2wjqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25546.006 Da / Num. of mol.: 1 / Fragment: unp residues 21-236 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dickeya dadantii (bacteria) / Strain: 3937 / Gene: kdgM, Dda3937_03362 / Plasmid: pKSM717 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)omp8/pLys / References: UniProt: Q934G3 | ||||
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#2: Chemical | #3: Chemical | ChemComp-C8E / ( #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M MES, 22% MPD, 36mM digalacturonate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.008 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 61216 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.93→49.36 Å / Num. obs: 16187 / % possible obs: 99.94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.78 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.4549 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2wjq Resolution: 1.93→15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.628 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.7 Å2 / Biso mean: 33.024 Å2 / Biso min: 5.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.908→1.957 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 8.09 Å / Origin y: 1.541 Å / Origin z: 2.228 Å
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Refinement TLS group |
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